3DGP | pdb_00003dgp

Crystal Structure of the complex between Tfb5 and the C-terminal domain of Tfb2


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1EVAPORATION8.9277Tris 20 mM, NaCl 50 mM, pH 8.9, EVAPORATION, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.0659.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.992α = 90
b = 99.992β = 90
c = 37.262γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152007-07-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.9198ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.85098.50.062610.3200321973723
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.870.9370.2490.2497.38.12181

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT1.8502003218822100699.10.199050.197070.20.237080.23RANDOM27.407
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
1.120.561.12-1.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.302
r_dihedral_angle_4_deg20.909
r_dihedral_angle_3_deg13.803
r_dihedral_angle_1_deg5.053
r_scangle_it3.95
r_scbond_it2.454
r_mcangle_it1.66
r_angle_refined_deg1.27
r_mcbond_it0.975
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.302
r_dihedral_angle_4_deg20.909
r_dihedral_angle_3_deg13.803
r_dihedral_angle_1_deg5.053
r_scangle_it3.95
r_scbond_it2.454
r_mcangle_it1.66
r_angle_refined_deg1.27
r_mcbond_it0.975
r_nbtor_refined0.303
r_symmetry_vdw_refined0.22
r_nbd_refined0.204
r_xyhbond_nbd_refined0.153
r_symmetry_hbond_refined0.129
r_chiral_restr0.097
r_bond_refined_d0.013
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1017
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DNAdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing